Many human diseases are associated with alleles that can be as simple as single-nucleotide changes to copy-number variants, gene fusions and translocations. The wealth of recent whole-genome sequencing has led to the realization that recent mutation play as important a role as variations that arose in distant ancestors. These disease-associated alleles can arise from mutational events that are provoked by errors arising In a number of ways during DNA replication, including (a) ionizing radiation, (b) the excision of mobile genetic elements, (c) the formation of double strand breaks (DSBs) at stalled replication forks, (d) replication slippage in DNA sequences that form alternative secondary structures, (e) conflicts between replication forks and the transcription machinery, and (f) the filling-in of singe-stranded DNA. This Program Project focuses on these different sources of mutation in a highly interactive set of projects that link researchers at Brandeis University and Tufts University studying three powerful model organisms: the bacterium pound coli, the single cell eukaryote, the budding yeast S. cerevisiae, and the metazoan, fruit fly D. melanogaster. Our goal is to understand in great detail the way several important types of mutations arise and to identify transcription, replication and DNA repair factors whose defects elevate their appearance. Importantly, the proposed core facilities will enable us to expand our studies beyond what has been previously possible and to test our models on genome-wide scales. Through the Core Facilities proposed as an integral part of this Program Project, participants will apply state-of-the-art high-throughput technologies to their studies of repair-associated mutagenesis. Automation of data collection and analysis will enable each investigator to expand the scope of their Investigation and will establish new standard procedures for the study of mutation generation. Interactions will be fostered by bi-monthly meetings of the entire labs from the two institutions, as well as at a retreat attended by two outside expert advisors.